Using competitive service Magics (check online if you can find mini magics, I think that´s a free version) I fixed your model.
It wasn´t quick and easy though because the model was terrible. The final model you deliver does have to be one solid part/shell
without intersecting triangles.
However if you use a tool like magics then often the easier strategy is to make separate parts (each of which has to be solid!) and use the excellent boolean tool in magics to unite everything into one solid part. However, if you do that then make sure that your seperate parts intersect (intersect! not overlap) so you can unite them.
One other thing, you can use Rhino but generally you are better off using polygon modelling software such as 3DS Max, Cinema4D, Maya, Blender etc. For the simple reason that polygons are triangles (or quadrangles or ngons, but these in turn consist of triangles) and that is exactly what an .stl file is made of. Rhino, Solidworks, Alias Autostudio etc. are all Nurbs based modellers.
One other thing about the pencilholder model: the scale is off by miles. Please check the images and let me know what the size has to be so I can resize the model and upload it back to you
.